Just a quick shot into the dark ...
it seems that this FFMPEG version applies "encoder=Lavc57.16.101 libtheora" too (for the embedded cover picture), instead of alone "Xiphophorus libVorbis", when having parameter on the cmdline: -codec:a libvorbis.
Although displayed on the screen log output, existing tag-data will be not transferred.
It seems like a problem in the FFMPEG recoding process or in the cmdline options???
But ... recoding a given ogg file ...
ffmpeg.exe -i "beanbonus.ogg" -codec:a libvorbis "bb2.ogg"
... creates a new ogg file with a tag-field:
ENCODER: Lavc57.16.101 libvorbis
... this seems to be ok, ...
and Mp3tag can work with this file.
DD.20151204.1234.CET
EDIT
This sequence of two ffmpeg.exe commands does work ...
ffmpeg.exe -i "Soundfile.mp3" "Soundfile.wav"
ffmpeg.exe -i "Soundfile.wav" -codec:a libvorbis "Soundfile.ogg"
... and Mp3tag does accept "Soundfile.ogg".
DD.20151204.1801.CET
EDIT
These piped ffmpeg.exe commands does work ...
ffmpeg.exe -i "Soundfile.mp3" -f wav -|ffmpeg.exe -i - -c:a libvorbis "Soundfile.ogg"
... and Mp3tag does accept "Soundfile.ogg".
DD.20151204.1819.CET
EDIT
These piped ffmpeg.exe commands does work ...
ffmpeg.exe -i "Soundfile.mp3" -f wav -|ffmpeg.exe -i - -c:a opus "Soundfile.opus"
... or ...
ffmpeg.exe -i "Soundfile.mp3" -f wav -|ffmpeg.exe -i - -c:a libopus "Soundfile.opus"
... and Mp3tag does accept "Soundfile.opus".
DD.20151205.1117.CET
EDIT
This standard ffmpeg.exe command does work ...
ffmpeg.exe -i "Soundfile.mp3" -c:a libopus "Soundfile.opus"
... and Mp3tag does accept "Soundfile.opus".
DD.20151205.1126.CET